Quality of random number generators significantly affects results of Monte Carlo simulations for organic and biological systems

We have simulated pure liquid butane, methanol, and hydrated alanine polypeptide with the Monte Carlo technique using three kinds of random number generators (RNG's)—the standard Linear Congruential Generator (LCG), a modification of the LCG with additional randomization used in the BOSS software, and the “Mersenne Twister” generator by Matsumoto and Nishimura. While using the latter two RNG's leads to reasonably similar physical features, the LCG produces significant different results. For the pure fluids, a noticeable expansion occurs. Using the original LCG on butane yields, a molecular volume of 171.4 ų per molecule compared to about 163.6–163.9 ų for the other two generators, a deviation of about 5%. For methanol, the LCG produces an average volume of 86.3 ų per molecule, which is about 24% higher than the 68.8–70.2 ų obtained with the RNG's in BOSS and the generator by Matsumoto and Nishimura. In case of the hydrated tridecaalanine peptide, the volume and energy tend to be noticeably greater with the LCG than with the BOSS (modified LCG) RNG's. For the simulated hydrated extended conformation of tridecaalanine, the difference in volume reached about 87%. The uniformity and periodicity of the generators do not seem to play the crucial role in these phenomena. We conclude that, it is important to test a RNG's by modeling a system such as the pure liquid methanol with a well‐established force field before routinely employing it in Monte Carlo simulations. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

New basis sets for the evaluation of interaction‐induced electric properties in hydrogen‐bonded complexes

Interaction‐induced static electric properties, that is, dipole moment, polarizability, and first hyperpolarizability, of the CO? (HF)_n and N₂? (HF)_n, n = 1–9 hydrogen‐bonded complexes are evaluated within the finite field approach using the Hartree–Fock, density functional theory, Møller–Plesset second‐order perturbation theory, and coupled cluster methods, and the LPol‐n (n = ds, dl, fs, fl) basis sets. To compare the performance of the different methods with respect to the increase of the complex size, we consider as model systems linear chains of the complexes. We analyze the results in terms of the many‐body and cooperative effects. © 2012 Wiley Periodicals, Inc.     

Ab initio prediction of the vibrational spectra of the hydrogen‐bonded complexes between CO and HONO2

The vibrational characteristics (vibrational frequencies and infrared intensities) for free and complexed CO and HONO₂ have been predicted using ab initio calculations at SCF and MP2 levels with different basis sets and B3LYP/6?31G(d,p) calculations. The ab initio calculations show that the complexation between HONO₂ and CO leads to two stable structures: CO … HONO₂ (1A) and OC … HONO₂ (1B). The changes in the vibrational characteristics from free monomers to complexes have been estimated. It was established that the most sensitive to the complexation is the stretching O? H vibration. In agreement with the experiment, its vibrational frequency in the complexes is shifted to lower frequency (Δν = ?123 cm^?1). The magnitude of the wave number shift is indicative of relatively strong hydrogen‐bonded interaction. The ab initio calculations at different levels predict an increase of the infrared intensity of the stretching O? H vibration for structure 1A more than five times and for structure 1B more than nine times. The most consistent agreement between the computed values of the frequency shifts for structure 1B and those experimentally observed suggests that this structure is preferred. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

Implicit and explicit solvent models for modeling a bifunctional arene ruthenium hydrogen‐storage catalyst: A classical and ab initio molecular simulation study

Classical and ab initio, density functional theory‐ and semiempirical‐based molecular simulation, including molecular dynamics, have been carried out to compare and contrast the effect of explicit and implicit solvation representation of tetrahydrofuran (THF) solvent on the structural, energetic, and dynamical properties of a novel bifunctional arene ruthenium catalyst embedded therein. Particular scrutiny was afforded to hydrogen‐bonding and energetic interactions with the THF liquid. It was found that the presence of explicit THF solvent molecules is required to capture an accurate picture of the catalyst's structural properties, particularly in view of the importance of hydrogen bonding with the surrounding THF molecules. This has implications for accurate modeling of the reactivity of the catalyst. © 2014 Wiley Periodicals, Inc.     

Time‐dependent density functional theory study on the absorption spectrum of Coumarin 102 and its hydrogen‐bonded complexes

The effect of both solvent polarity and hydrogen bonding (HB) on the electronic transition energy of Coumarin 102 (C102) has been examined using the time‐dependent density functional theory (TDDFT). Solvent effect on both geometry and electronic transition energy is evaluated using the polarizable continuum model (PCM). A linear relation of the absorption maximum of C102 with the solvent polarity function Δf is found using the TDDFT‐PCM method for all solvents except dimethyl sulfoxide. The solvent polarity and the type B HB between the carbonyl oxygen and solvent hydrogen atom make the absorption wavelength redshift, whereas the type A HB between the amino nitrogen atom and solvent hydrogen atom has an opposite effect on the absorption wavelength. The calculated absorption wavelengths of C102 with two type B HB between the carbonyl oxygen and solvent hydrogen atom are in excellent agreement with experimental measurements. The solvatochromism of C102 is analyzed in terms of the Kamlet–Taft equation and the parameters s and a are discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.     

Three closely related dibenzazepine carboxylic acids: hydrogen‐bonded aggregation in one,two and three dimensions

In the structure of (6R*,11R*)‐5‐acetyl‐11‐ethyl‐6,11‐dihydro‐5H‐dibenzo[b,e]azepine‐6‐carboxylic acid, C₁₉H₁₉NO₃, (I), the molecules are linked into sheets by a combination of O—H...O and C—H...O hydrogen bonds; in the structure of the monomethyl analogue (6RS,11SR)‐5‐acetyl‐11‐ethyl‐2‐methyl‐6,11‐dihydro‐5H‐dibenzo[b,e]azepine‐6‐carboxylic acid, C₂₀H₂₁NO₃, (II), the molecules are linked into simple C(7) chains by O—H...O hydrogen bonds; and in the structure of the dimethyl analogue (6RS,11SR)‐5‐acetyl‐11‐ethyl‐1,3‐dimethyl‐6,11‐dihydro‐5H‐dibenzo[b,e]azepine‐6‐carboxylic acid, C₂₁H₂₃NO₃, (III), a combination of O—H...O, C—H...O and C—H...π(arene) hydrogen bonds links the molecules into a three‐dimensional framework structure. None of these structures exhibits the R₂²(8) dimer motif characteristic of simple carboxylic acids.     

Effect of hydrogen‐bonded interactions on the energetics and spectral properties of the astromolecule aminoacetonitrile

A detailed and systematic electronic structure calculation has been performed to analyze the hydrogen‐bonded interaction of aminoacetonitrile (H₂NCH₂CN) with hydrogen cyanide (HCN) and Glycine (H₂NCH₂COOH). Both HCN and aminoacetonitrile have already been detected in the interstellar medium (ISM) and their active role in the molecular mechanisms of glycine production has already been recognized. Four different density functional models have been used to study the effect of hydrogen bond formation on the energetic stability and vibrational spectra of the aminoacetonitrile‐HCN and aminoacetonitrile‐glycine complexes in gas phase. The aminoacetonitrile‐glycine dimer is energetically far more stable than all forms of aminoacetonitrile‐HCN dimers. Elastic and inelastic scattering of light off the hydrogen‐bonded clusters have been investigated in details via Rayleigh and Raman spectroscopic parameters. The dipole moments and depolarization ratios are found to be sensitive on the type of hydrogen‐bond network. The mean polarizabilty show appreciable dependence on the choice of the DFT‐model. In general, all the chemical groups (OH, CN, NH₂, and CH) that participate directly in the hydrogen bond formation suffer appreciable variation in the intensity of vibration.     

Topological study of diverse hydrogen‐bonded patterns found in a system of a nickel(II) complex and the sulfate anion

A nickel(II) coordination complex, bis[2,6‐bis(1H‐benzimidazol‐2‐yl‐κN³)pyridine‐κN]nickel(II) sulfate, [Ni(C₁₉H₁₃N₅)₂]SO₄ or [Ni(H₂L)₂]SO₄, having four peripheral tetrahedrally oriented N—H donor units, combines with sulfate bridges to create hydrogen‐bonded structures of varied dimensionality. The three crystal structures reported herein in the space groups P2₁2₁2₁, I and Pccn are defined solely by strong charge‐assisted N—H…O hydrogen bonds and contain disordered guests (water and dimethylformamide) that vary in size, shape and degree of hydrophilicity. Two of the compounds are channelled solids with three‐dimensional structures, while the third is one‐dimensional in nature. In spite of their differences, all three present a striking resemblance to the previously reported anhydrous relative [Guo et al. (2011). Chin. J. Inorg. Chem. 27 , 1517–1520], which is considered as the reference framework from which all three title compounds are derived. The hydrogen‐bonded frameworks are described and compared using crystallographic and topological approaches.     

Density functional studies on hydrogen‐bonded clusters of hydrogen halides and the interaction on halide anions

Density functional theory (DFT) calculations have been performed to study the structures and stability of X^?·(HX)_n=2–5 clusters where X = F, Cl, Br at B3LYP/6‐311++G** level of theory. The presence of halide ions in these clusters disintegrates the hydrogen halide clusters. All the hydrogen halides are then hydrogen bonded to the centrally placed halide ions, thereby forming multiple hydrogen bonds. The interaction energies have been corrected for the basis set superposition error (BSSE) using Boy's counterpoise correction method. Evidence for the destruction of hydrogen bonds in hydrogen halide clusters due to the presence of halide ions is further obtained from topological analysis and natural bond orbital analysis. The chemical hardness and chemical potential have been calculated for all the anion clusters. The above analysis reveals that hydrogen bonding in these systems is not an essentially electrostatic interaction. The nature of the stabilization interactions operative in these multiple hydrogen‐bonded clusters has been explained in terms of many‐body contribution to interaction energies. From these studies, an attempt has been made to understand the nature of the molecular properties resulting from different electronegativities of the halogens. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Hydrogen‐bonded two‐ and three‐dimensional polymeric structures in the ammonium salts of 3,5‐dinitrobenzoic acid, 4‐nitrobenzoic acid and 2,4‐dichlorobenzoic acid

The structures of ammonium 3,5‐dinitrobenzoate, NH₄⁺·C₇H₃N₂O₆⁻, (I), ammonium 4‐nitrobenzoate dihydrate, NH₄⁺·C₇H₄NO₄⁻·2H₂O, (II), and ammonium 2,4‐dichlorobenzoate hemihydrate, NH₄⁺·C₇H₃Cl₂O₂⁻·0.5H₂O, (III), have been determined and their hydrogen‐bonded structures are described. All three salts form hydrogen‐bonded polymeric structures, viz. three‐dimensional in (I) and two‐dimensional in (II) and (III). With (I), a primary cation–anion cyclic association is formed [graph set R₄³(10)] through N—H...O hydrogen bonds, involving a carboxylate group with both O atoms contributing to the hydrogen bonds (denoted O,O′‐carboxylate) on one side and a carboxylate group with one O atom involved in two hydrogen bonds (denoted O‐carboxylate) on the other. Structure extension involves N—H...O hydrogen bonds to both carboxylate and nitro O‐atom acceptors. With structure (II), the primary inter‐species interactions and structure extension into layers lying parallel to (001) are through conjoined cyclic hydrogen‐bonding motifs, viz.R₄³(10) (one cation, an O,O′‐carboxylate group and two water molecules) and centrosymmetric R₄²(8) (two cations and two water molecules). The structure of (III) also has conjoined R₄³(10) and centrosymmetric R₄²(8) motifs in the layered structure but these differ in that the first motif involves one cation, an O,O′‐carboxylate group, an O‐carboxylate group and one water molecule, and the second motif involves two cations and two O‐carboxylate groups. The layers lie parallel to (100). The structures of salt hydrates (II) and (III), displaying two‐dimensional layered arrays through conjoined hydrogen‐bonded nets, provide further illustration of a previously indicated trend among ammonium salts of carboxylic acids, but the anhydrous three‐dimensional structure of (I) is inconsistent with that trend.     

On the choice of a reference state for one‐step perturbation calculations between polar and nonpolar molecules in a polar environment

One‐step perturbation is an efficient method to estimate free energy differences in molecular dynamics (MD) simulations, but its accuracy depends critically on the choice of an appropriate, possibly unphysical, reference state that optimizes the sampling of the physical end states. In particular, the perturbation from a polar moiety to a nonpolar one and vice versa in a polar environment such as water poses a challenge which is of importance when estimating free energy differences that involve entropy changes and the hydrophobic effect. In this work, we systematically study the performance of the one‐step perturbation method in the calculation of the free enthalpy difference between a polar water solute and a nonpolar “water” solute molecule solvated in a box of 999 polar water molecules. Both these polar and nonpolar physical reference states fail to predict the free enthalpy difference as obtained by thermodynamic integration, but the result is worse using the nonpolar physical reference state, because both a properly sized cavity and a favorable orientation of the polar solute in a polar environment are rarely, if ever, sampled in a simulation of the nonpolar solute in such an environment. Use of nonphysical soft‐core reference states helps to sample properly sized cavities, and post‐MD simulation rotational and translational sampling of the solute to be perturbed leads to much improved free enthalpy estimates from one‐step perturbation. © 2012 Wiley Periodicals, Inc.     

Nuclear quantum effect and temperature dependency on the hydrogen‐bonded structure of base pairs

The structure of Watson–Crick‐type adenine‐thymine and guanine‐cytosine pairs has been studied by hybrid Monte Carlo (HMC) and path integral hybrid Monte Carlo (PIHMC) simulations with the use of semiempirical PM6‐DH+ method in the gas phase. We elucidated the nuclear quantum effect and temperature dependency on the hydrogen‐bonded moiety of base pairs. It was shown that the contribution of nuclear quantum effect on the hydrogen‐bonded structure is significant not only at low temperature 150 K but also at temperature as high as 450 K. The relative position of hydrogen‐bonded proton between two heavy atoms and the nuclear quantum nature of the proton are also shown. Furthermore, we have applied principal component analysis to HMC and PIHMC simulations to analyze the nuclear quantum effect on intermolecular motions. We found that the ratio of Buckle mode (lowest vibrational mode from normal mode analysis) decreases due to the nuclear quantum effect, whereas that of Propeller mode (second lowest vibrational mode) increases. In addition, nonplanar structures of base pairs were found to become stable due to the nuclear quantum effect from two‐dimensional free energy landscape along Buckle and Propeller modes. © 2013 Wiley Periodicals, Inc.     

Fracture behavior of triglyceride‐based adhesives

The use of natural plant oils in the production of adhesives has been the focus of much research because natural oils are a renewable resource which have environmental and economic advantages over the petroleum‐derived chemicals used in traditional adhesives. The network formation and the stress–strain behavior of these plant oil–based adhesives is studied using a combination of simulation techniques. An off‐lattice Monte Carlo simulation has been developed to model the formation of these networks via the free‐radical copolymerization of the triglycerides present in natural oils. Networks of systems representing the triglycerides found in soybean oil, linseed oil, and olive oil are generated, as are networks made from other “theoretical” natural oils. The structure of the networks is characterized by percolation analysis. The stress–strain behavior of these networks is studied using large‐scale molecular dynamics simulations. Tensile strains are applied to the networks and it is observed that with increasing n the failure stress increases but the failure strain decreases. Also, for systems with low values of n, large voids form while the system is strained and then the system fails cohesively. However, for large n, no significant voiding is observed and the system fails close to the interface. The simulation results are shown to be consistent with the vector percolation theoretical prediction for how the failure stress relates to n. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3333–3343, 2004     

Elastic models,lattice dynamics and finite size effects in molecular spin crossover systems

The experimental studies of spin-crossover compounds switched in the last decade from bulk measurements and macroscopic observations to the nanoscale and microscopic approaches. In this context, new and sometimes unexpected behaviours have been documented, which could be partially described only by the classical phenomenological models developed in the last period of the last century. In this context, the development of more complex models, able to reproduce the nucleation and domain propagation within the material, has proved to be not a whim of some theoreticians but a necessity, which facilitated the full understanding of observed phenomena and even made premises for further experiments. Here, we present and analyse various elastic models identifying their common points and differences and discuss how they can be used for the study of microscopic phenomena as the cluster formation, stability and propagation or for the study of finite size effects in spin-crossover nanoparticles, with open boundary conditions or embedded in various matrices.     

Effect of Protic Ionic Liquid and Surfactant Structure on Partitioning of Polyoxyethylene Non‐ionic Surfactants

The partitioning constants and Gibbs free energies of transfer of poly(oxyethylene) n‐alkyl ethers between dodecane and the protic ionic liquids (ILs) ethylammonium nitrate (EAN) and propylammonium nitrate (PAN) are determined. EAN and PAN have a sponge‐like nanostructure that consists of interpenetrating charged and apolar domains. This study reveals that the ILs solvate the hydrophobic and hydrophilic parts of the amphiphiles differently. The ethoxy groups are dissolved in the polar region of both ILs by means of hydrogen bonds. The environment is remarkably water‐like and, as in water, the solubility of the ethoxy groups in EAN decreases on warming, which underscores the critical role of the IL hydrogen‐bond network for solubility. In contrast, amphiphile alkyl chains are not preferentially solvated by the charged or uncharged regions of the ILs. Rather, they experience an average IL composition and, as a result, partitioning from dodecane into the IL increases as the cation alkyl chain is lengthened from ethyl to propyl, because the IL apolar volume fraction increases. Together, these results show that surfactant dissolution in ILs is related to structural compatibility between the head or tail group and the IL nanostructure. Thus, these partitioning studies reveal parameters for the effective molecular design of surfactants in ILs.